{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0649NZHX/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0649NZHX",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinB_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0649NZHX](/measurement-sets/IGVFDS0649NZHX/) has in progress subobject auxiliary set [IGVFDS4408NUQV](/auxiliary-sets/IGVFDS4408NUQV/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0649NZHX/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6784MZOT](/in-vitro-systems/IGVFSM6784MZOT/) has in progress subobject construct library set [IGVFDS2385DHZO](/construct-library-sets/IGVFDS2385DHZO/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM6784MZOT/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0649NZHX](/measurement-sets/IGVFDS0649NZHX/) has no cell sorting `auxiliary_sets`. CRISPR-based measurement sets that utilize flow cytometry are expected to link to a cell sorting auxiliary set.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS0649NZHX/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS4408NUQV](/auxiliary-sets/IGVFDS4408NUQV/) has sequence file(s): [IGVFFI8239HVHU](/sequence-files/IGVFFI8239HVHU/), [IGVFFI3063NIHT](/sequence-files/IGVFFI3063NIHT/), [IGVFFI8619DYIT](/sequence-files/IGVFFI8619DYIT/), [IGVFFI3654HJBV](/sequence-files/IGVFFI3654HJBV/), [IGVFFI0116NIQJ](/sequence-files/IGVFFI0116NIQJ/), [IGVFFI7994RXZI](/sequence-files/IGVFFI7994RXZI/), [IGVFFI9339SLDF](/sequence-files/IGVFFI9339SLDF/), [IGVFFI3066LCET](/sequence-files/IGVFFI3066LCET/), [IGVFFI3837WDLK](/sequence-files/IGVFFI3837WDLK/), [IGVFFI1929VUST](/sequence-files/IGVFFI1929VUST/), [IGVFFI9123LEUC](/sequence-files/IGVFFI9123LEUC/), [IGVFFI1337EMZN](/sequence-files/IGVFFI1337EMZN/), [IGVFFI0624KKKY](/sequence-files/IGVFFI0624KKKY/), [IGVFFI6164VNIA](/sequence-files/IGVFFI6164VNIA/), [IGVFFI4693FJTS](/sequence-files/IGVFFI4693FJTS/), [IGVFFI8902DSVE](/sequence-files/IGVFFI8902DSVE/), [IGVFFI0067VSPN](/sequence-files/IGVFFI0067VSPN/), [IGVFFI4388AVGJ](/sequence-files/IGVFFI4388AVGJ/), [IGVFFI8586BVYX](/sequence-files/IGVFFI8586BVYX/), [IGVFFI4516KFGA](/sequence-files/IGVFFI4516KFGA/), [IGVFFI6525HRBA](/sequence-files/IGVFFI6525HRBA/), [IGVFFI3070BYXY](/sequence-files/IGVFFI3070BYXY/), [IGVFFI8959ACSK](/sequence-files/IGVFFI8959ACSK/), [IGVFFI9503OUYA](/sequence-files/IGVFFI9503OUYA/), [IGVFFI3654UMQO](/sequence-files/IGVFFI3654UMQO/), [IGVFFI6736WIXV](/sequence-files/IGVFFI6736WIXV/), [IGVFFI8889WEQZ](/sequence-files/IGVFFI8889WEQZ/), [IGVFFI9143KWLU](/sequence-files/IGVFFI9143KWLU/), [IGVFFI9823KTAK](/sequence-files/IGVFFI9823KTAK/), [IGVFFI4423OXOL](/sequence-files/IGVFFI4423OXOL/), [IGVFFI4199KVLO](/sequence-files/IGVFFI4199KVLO/), [IGVFFI3289BORC](/sequence-files/IGVFFI3289BORC/), [IGVFFI3455ITYP](/sequence-files/IGVFFI3455ITYP/), [IGVFFI8355YJTF](/sequence-files/IGVFFI8355YJTF/), [IGVFFI1184CQVO](/sequence-files/IGVFFI1184CQVO/), [IGVFFI0396DSME](/sequence-files/IGVFFI0396DSME/), [IGVFFI2236HMRF](/sequence-files/IGVFFI2236HMRF/), [IGVFFI0381FPNM](/sequence-files/IGVFFI0381FPNM/), [IGVFFI3761RNPN](/sequence-files/IGVFFI3761RNPN/), [IGVFFI5539BOBA](/sequence-files/IGVFFI5539BOBA/), [IGVFFI0941MYBB](/sequence-files/IGVFFI0941MYBB/), [IGVFFI8609TIHW](/sequence-files/IGVFFI8609TIHW/), [IGVFFI6944IORM](/sequence-files/IGVFFI6944IORM/), [IGVFFI6839COMN](/sequence-files/IGVFFI6839COMN/), [IGVFFI8731DWKI](/sequence-files/IGVFFI8731DWKI/), [IGVFFI1753SSFD](/sequence-files/IGVFFI1753SSFD/), [IGVFFI8836QTRR](/sequence-files/IGVFFI8836QTRR/), [IGVFFI7111CSTT](/sequence-files/IGVFFI7111CSTT/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS4408NUQV/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS4408NUQV](/auxiliary-sets/IGVFDS4408NUQV/) has sequence file(s) [IGVFFI8239HVHU](/sequence-files/IGVFFI8239HVHU/), [IGVFFI3063NIHT](/sequence-files/IGVFFI3063NIHT/), [IGVFFI8619DYIT](/sequence-files/IGVFFI8619DYIT/), [IGVFFI3654HJBV](/sequence-files/IGVFFI3654HJBV/), [IGVFFI0116NIQJ](/sequence-files/IGVFFI0116NIQJ/), [IGVFFI7994RXZI](/sequence-files/IGVFFI7994RXZI/), [IGVFFI9339SLDF](/sequence-files/IGVFFI9339SLDF/), [IGVFFI3066LCET](/sequence-files/IGVFFI3066LCET/), [IGVFFI3837WDLK](/sequence-files/IGVFFI3837WDLK/), [IGVFFI1929VUST](/sequence-files/IGVFFI1929VUST/), [IGVFFI9123LEUC](/sequence-files/IGVFFI9123LEUC/), [IGVFFI1337EMZN](/sequence-files/IGVFFI1337EMZN/), [IGVFFI0624KKKY](/sequence-files/IGVFFI0624KKKY/), [IGVFFI6164VNIA](/sequence-files/IGVFFI6164VNIA/), [IGVFFI4693FJTS](/sequence-files/IGVFFI4693FJTS/), [IGVFFI8902DSVE](/sequence-files/IGVFFI8902DSVE/), [IGVFFI0067VSPN](/sequence-files/IGVFFI0067VSPN/), [IGVFFI4388AVGJ](/sequence-files/IGVFFI4388AVGJ/), [IGVFFI8586BVYX](/sequence-files/IGVFFI8586BVYX/), [IGVFFI4516KFGA](/sequence-files/IGVFFI4516KFGA/), [IGVFFI6525HRBA](/sequence-files/IGVFFI6525HRBA/), [IGVFFI3070BYXY](/sequence-files/IGVFFI3070BYXY/), [IGVFFI8959ACSK](/sequence-files/IGVFFI8959ACSK/), [IGVFFI9503OUYA](/sequence-files/IGVFFI9503OUYA/), [IGVFFI3654UMQO](/sequence-files/IGVFFI3654UMQO/), [IGVFFI6736WIXV](/sequence-files/IGVFFI6736WIXV/), [IGVFFI8889WEQZ](/sequence-files/IGVFFI8889WEQZ/), [IGVFFI9143KWLU](/sequence-files/IGVFFI9143KWLU/), [IGVFFI9823KTAK](/sequence-files/IGVFFI9823KTAK/), [IGVFFI4423OXOL](/sequence-files/IGVFFI4423OXOL/), [IGVFFI4199KVLO](/sequence-files/IGVFFI4199KVLO/), [IGVFFI3289BORC](/sequence-files/IGVFFI3289BORC/), [IGVFFI3455ITYP](/sequence-files/IGVFFI3455ITYP/), [IGVFFI8355YJTF](/sequence-files/IGVFFI8355YJTF/), [IGVFFI1184CQVO](/sequence-files/IGVFFI1184CQVO/), [IGVFFI0396DSME](/sequence-files/IGVFFI0396DSME/), [IGVFFI2236HMRF](/sequence-files/IGVFFI2236HMRF/), [IGVFFI0381FPNM](/sequence-files/IGVFFI0381FPNM/), [IGVFFI3761RNPN](/sequence-files/IGVFFI3761RNPN/), [IGVFFI5539BOBA](/sequence-files/IGVFFI5539BOBA/), [IGVFFI0941MYBB](/sequence-files/IGVFFI0941MYBB/), [IGVFFI8609TIHW](/sequence-files/IGVFFI8609TIHW/), [IGVFFI6944IORM](/sequence-files/IGVFFI6944IORM/), [IGVFFI6839COMN](/sequence-files/IGVFFI6839COMN/), [IGVFFI8731DWKI](/sequence-files/IGVFFI8731DWKI/), [IGVFFI1753SSFD](/sequence-files/IGVFFI1753SSFD/), [IGVFFI8836QTRR](/sequence-files/IGVFFI8836QTRR/), [IGVFFI7111CSTT](/sequence-files/IGVFFI7111CSTT/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 40,
"level_name": "WARNING",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS4408NUQV/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS4408NUQV](/auxiliary-sets/IGVFDS4408NUQV/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_file_set_for",
"path": "/auxiliary-sets/IGVFDS4408NUQV/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS4408NUQV/",
"accession": "IGVFDS4408NUQV",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinB_AmpliconSequencing_AuxiliarySet"
],
"file_set_type": "variant sequencing"
}
],
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
"control_file_sets": [
{
"@id": "/measurement-sets/IGVFDS5128CXIS/",
"accession": "IGVFDS5128CXIS",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-13T08:01:36.603889+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
"files": [],
"input_file_set_for": [
"/analysis-sets/IGVFDS4359OODY/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set.",
"preferred_assay_title": "Variant FlowFISH",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"release_timestamp": "2023-12-20T23:08:08.505904+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6784MZOT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6784MZOT",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinB"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2385DHZO/",
"accession": "IGVFDS2385DHZO",
"file_set_type": "guide library",
"summary": "Guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
}
],
"status": "released",
"summary": "THP-1 cell line, male, Homo sapiens (sorting details: FACS bin for 26-50% expression of PPIF) modified with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "21",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-13T08:16:35.901241+00:00",
"summary": "Variant FlowFISH integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000108179/",
"geneid": "ENSG00000108179",
"name": "peptidylprolyl isomerase F",
"symbol": "PPIF",
"synonyms": [
"rotamase F",
"CYP3",
"cyclophilin F",
"mitochondrial cyclophilin",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"CypD",
"Cyp-D",
"cyclophilin 3",
"cyclophilin D",
"CyP-M",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIase F"
]
}
],
"uuid": "a2463aed-33e7-4921-ab0f-f8782a40144c"
}